gromacs-2018.4-bp152.3.56

- version bump to 2018.4 details here:
  http://manual.gromacs.org/documentation/2018.4/release-notes/2018/2018.4.html
  Highlights:
  - Correct PME forces with free energy without perturbed charges/LJ
  - Add constraint contribution to foreign Hamiltonian differences
  - Add mass contribution to foreign Hamiltonian differences
  - Work around bugs with expanded ensemble runs
  - Checkpoint continuations require suitable .tpr files
  - Fix mindist output file checks
  - Fix gmx helix segmentation faults
  - Fix bug in entropy calculation in gmx anaeig
  - Fixed an issue where the log file could sometimes report an incorrect initial dynamic load balancing state
  - Fix Bromine parameters in amber forcefield files
  - Made normal-mode analysis work for more than one molecule
  - Disallow rerun using same filename as output file
  - Fix issue when building GROMACS without TNG

- version bump to 2018.3 details here:
  http://manual.gromacs.org/documentation/2018.3/release-notes/2018/2018.3.html
  Highlights:
  - Multi-domain GPU runs can no longer miss pair interactions
  - Fix Conjugate Gradient assertion failure at end of minimization
  - Multi-domain Conjugate Gradient minimimization no longer segfaults.
  - Fix pairlist buffer with Brownian Dynamics
  - Avoid ?atom moved to far? errors
  - grompp now checks that pull groups are not close to half the box size
  - Fixed segmentation fault in mdrun with QM/MM ONIOM scheme
  - Fixed syntax error in make_gromos_rtp.py
  - Fix gmx solvate topology updating
  - Fix bfactor output error caused by fix for Issue 2511
  - Made sure that gmx rms can skip values
  - Fix trjconv when not providing structure file
  - Fix enforced rotation energy output
  - Fix nvcc host compiler check triggering
  - Report up to date hwloc version information
  - Disable single compilation unit with CUDA 9.0
  - Avoid aborting mdrun when GPU sanity check detects errors
  - Improve OpenCL kernel performance on AMD Vega GPUs

- version bump to 2018.2 details here:
  http://manual.gromacs.org/documentation/2018.2/release-notes/2018/2018.2.html
  Highlights:
  - Prevented OpenCL timing memory leak
  - Fixed MPI error after constraint failure during energy minimization
  - Fixed moving frozen atoms with constraints
  - Fixed COM removal moving frozen atoms

- version bump to 2018.1 details here:
  http://manual.gromacs.org/documentation/2018.1/release-notes/2018/2018.1.html
  Highlights:
  - Fixed leap-frog integrator with Nose-Hoover T coupling and Parrinello-Rahman P coupling
  - Used SIMD bondeds without perturbed interactions
  - Fixed bonds whose displacement was zero
  - Fixed centre-of-mass motion removal on part of the system
  - Fixed multi-simulations with multiple ranks per simulation
  - Improved inter-simulation signalling implementation
  - Fixed FEP calculations with SHAKE
  - Fixed handling of mdp define statement assigning preprocessor values
  - Prevented log file energy average printing dividing by zero

- Add _constraints file to avoid build failure and timeout on tests
  for slow CPU workers

- version bump to 2018 details here:
  http://manual.gromacs.org/documentation/2018/ReleaseNotes/index.html
  Highlights:
  - A new dual-list dynamic-pruning algorithm for the short-ranged interactions
  - PME long-ranged interactions can now run on a single GPU
  - AWH (Accelerated Weight Histogram) method is now supported
  - A physical validation suite is added, which runs a series of short simulations
  - Conserved quantities are computed and reported for more integration schemes
- disable GPU on ppc64le, build error
- use internal tinyxml2 as tinxml-6 is broken with gromacs, only testing is build it anyhow

- enable GPU support via OpenCL

- adapt to new openlmi package - source mpivars.h during build

- version bump to 2016.4 details here:
  http://manual.gromacs.org/documentation/2016.4/ReleaseNotes/index.html
  Highlighs:
  - Disabled PME tuning with the group scheme
  - Fixed value of Ewald shift
  - Fixed orientation restraint reference
  - Fixed bugs with setup for orientation restraints
  - Worked around missing OpenMP implementation in orientation restraints
  - Enable group-scheme SIMD kernels on recent AVX extensions
  - Fix FEP state with rerun
  - Fixed COM pull force with SD
  - Fix PBC bugs in the swap code
  - Fixed flat-bottomed position restraints with multiple ranks
  - Fixed null pointer print in DD
  - Improved the ?files not present? error message
  - Fixed LJ-PME + switch grompp error
  - Fixed unused SIMD PME table kernel
  - Fixed bugs in most double-precision Simd4 implementations
  - Avoid inf in SIMD double sqrt()
  - Fix NVML error messages
  - Fixed IMD interface malfunctions
  - Fixed initial temperature reporting
  - Fix exception in SIMD LJ PME solve

- Fix build on Factory

- __builddir is not overwritable on SLE-12, so use subdirs
- disable test on s390x (too slow)

- version bump to 2016.3 details here:
  http://manual.gromacs.org/documentation/2016.1/ReleaseNotes/index.html
- Highlights:
  - Made distance restraints work with threads and DD
  - Fixed Ewald surface+3DC corrections
  - Fixed opening of wall table files
  - Fixed bug in gmx insert-molecules.
  - Made virial reproducible
  - Updated to support FFTW 3.3.5
  - Permitted automatic load balancing to disable itself when it makes the run slower
  - Improved the accuracy of timing for dynamic load balancing with GPUs
  - Corrected kernel launch bounds for Tesla P100 GPUs
  - Improved logic handling if/when the run is terminated for SETTLE warnings
  - Fixed bug in gmx wham for reading pullx files.
  - Fixed ouput bug in gmx wham
  - Fixed deadlock with thread-MPI
  - Made error reporting in grompp more user friendly
  - Fixed SIMD suggestion for VMX
  - Fixed script xplor2gmx.pl to work with GMXDATA
  - Fixed default nice level in mdrun-only build
  - Fixed math-test false positive
  - Improved documentation
  - OpenCL error string are now written, instead of cryptic error codes
  - Fixed build with GMX_USE_TNG=off
  - Removed variable-precision .gro writing
  - Fixed BG/Q platform files and install guide
  - Reduced the memory required for free-energy simulations

- version bump to 2016.1 details here:
  http://manual.gromacs.org/documentation/2016/ReleaseNotes/index.html
- Highlights:
  - Made distance restraints work with threads and DD
  - Fixed Ewald surface+3DC corrections
  - Fixed opening of wall table files
  - Fixed bug in gmx insert-molecules.
  - Made virial reproducible
  - Permitted automatic load balancing to disable itself when it makes the run slower
  - Improved the accuracy of timing for dynamic load balancing with GPUs
  - Corrected kernel launch bounds for Tesla P100 GPUs
  - Improved logic handling if/when the run is terminated for SETTLE warnings
  - Fixed bug in gmx wham for reading pullx files.
  - Fixed ouput bug in gmx wham
  - Fixed deadlock with thread-MPI
  - Made error reporting in grompp more user friendly
  - Fixed SIMD suggestion for VMX
  - Fixed script xplor2gmx.pl to work with GMXDATA
  - Fixed default nice level in mdrun-only build
  - Fixed math-test false positive
  - Improved documentation
  - Fixed build with GMX_USE_TNG=off
  - Removed variable-precision .gro writing
  - Reduced the memory required for free-energy simulations

- version bump to 2016 details here:
  http://manual.gromacs.org/documentation/2016/ReleaseNotes/index.html
- Highlights:
  - As always, we?ve got several useful performance improvements, with or without GPUs. CPU-side SIMD and threading enhancements will make GPU-accelerated simulations faster even if we?d left the GPU code alone! Thanks to these and additional GPU kernel improvements, in GPU-accelerated runs expect around 15% improvement in throughput. (And not just for plain vanilla MD, either... the pull code now supports OpenMP threading throughout, and multi-simulations have less coupling between simulations.)
  - We have a new C++11 portability layer permitting us to accelerate in SIMD on the CPU lots of minor routines. These will also often improve runs that use accelerators or many nodes through better load balancing. POWER8, ARM64, AVX512 (KNL), and more are fully SIMD accelerated now because they are supported in the new portability layer!
  - We made further SIMD acceleration of bonded interactions which reduces their calculation time by about a factor of 2. This improves load balance at high parallelization by a factor of 2, and shows significantly better scaling.
  - Similarly, SIMD acceleration of SETTLE reduces the time for constraints by a factor of 3 to 5 - which has a strong effect for GPU runs.
  - OpenCL GPU support is now available with all combinations of MPI, thread-MPI and GPU sharing (ie. the same as CUDA). Kernel performance has improved by up to 60%. AMD GPUs benefit the most, OpenCL on NVIDIA is generally still slow.
  - Tools in the new analysis framework can handle trajectories that are subsets of the simulation system.
  - New pull coordinate geometries angle-axis, dihedral, and normal angle.
  - Checkpoint restarts work only in the cases where the implementation can always do what the user wants.
  - The version numbering has changed to be the year of the release, plus (in future) a patch number. GROMACS 2016 will be the initial release from this branch, then GROMACS 2016.1 will have the set of bugs that have been fixed in GROMACS 2016, etc.

- version bump to 5.1 details here:
  http://manual.gromacs.org/documentation/5.1/ReleaseNotes/index.html
- html documentation is gone
- devel package now includes cmake macros and config files

- version bump to 5.0.2
- Details: http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x

- version bump to 5.0.1
- Details: http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x

- added %check

- version bumped to 4.6.5
- fix GMX_CPU_ACCELERATION to SSE2 for older i386 machines
- added openmpi package
- split doc, bash-completion into separate packages

- Update to 4.6.1
  Bugfix release
  - increased shared object major version to 8, #1147
  - updates to HTML manual, install guide, PDF manual, shell completions
    copious minor bug fixes
  - various build system upgrades and fixes #1143
  - new and enhanced error messages
  - fixes for AdResS bugs (neighbour list construction, flop accounting,
    multiple tf tables)
  - fixed PME timing counter issues #1125
  - fixed PME load balance reporting
  - fixed forcerec to work with tools like genion and g_disre #1136
  - various GPU performance enhancements
  - fixed sd integrator with OpenMP threading #1138
  - various minor fixes for interacting with CUDA for GPUs
  - fixes for g_tune_pme to cope with new mdrun behaviour and changed
    command-line options (for both g_tune_pme and mdrun)
  - more checks for system support for setting thread affinities
  - removed inter-flag dependency in g_order
  - fixed issues with free-energy pertubation soft-core and cut-offs #1146
  - fixed issues with md-vv + nose-hoover + (nstcalcenergy > nsttcouple)
    [#1129]
  - incorporated new changes from release 4.5.x branch
  - prevented building with icc 11.1 and SSE4.1 because of known problems
    [#1126]
  - adding warning about not building with icc version < 12 #1126
  - fixed bug sorting atoms with GPUs introduced since 4.6 #1153
  - fixed issues with automated download of regression tests #1150
  - fixed bug with DD cut-off check and PME dynamic load balancing #1169

- Update to 4.6
  New features
  - New Verlet non-bonded scheme which, by default, uses exact cut-off's
    and a buffered pair-list.
  - Multi-level hybrid parallelization (MPI + OpenMP + CUDA):
    full OpenMP multithreading with the Verlet scheme;
  - OpenMP mulitthreading for PME-only nodes with the group scheme;
    native GPU acceleration using CUDA (supporte NVIDIA hardware).
  - New x86 SIMD non-bonded kernels for the usual cut-off scheme, called
    group scheme and the new verlet scheme, use x86 SIMD intrinsics (no
    more assembly code):
    SSE2
    SSE4.1
    AVX-128-FMA (for AMD Bulldozer/Piledriver)
    AVX-256 (for Intel Sandy/Ivy Bridge)
  - Automated OpenMP thread count choice to use all available cores.
  - Automated CPU affinity setting: locking processes or threads to cores.
  - Automated PP-PME (task) load-balancing: balancing non-bonded force and
    PME mesh workload when the two are executed on different
    compute-resources (i.e CPU and GPU or different CPUs). This enables
    GPU-CPU and PP-PME process load balancing by shifting work from the
    mesh to the non-bonded calculation.
  - PPPM/P3M with analytical derivative at the same cost and with the same
    features as PME.
  - New, advanced free energy sampling techniques.
  - AdResS adaptive resolution simulation support.
  - Enforced rotation ("rotational pulling")
  - Build configuration now uses CMake, configure+autoconf/make no longer
    supported. (The CMake build system features with a lot of automation
    and cleverness under the hood and we know that the it might not always
    prove to be as rock-solid as the old one. However, far more advanced
    and complex, so bear with us while we iron out issues that come up
    along the way.)
  - g_hbond now utilizes OpenMP.
  Plus plenty of bug fixes.

- Clean up spec file

- Clean up spec file
- Update to 4.5.5
  - Improved pdb2gmx -chainsep option and reintroduced the -merge option.
  - Fixed mdrun file appending truncating files to 0 bytes when
    continuation runs stopped before writing new output.
  - Fixed COM pulling with multiple constraints checking the
    convergence of one constraint instead of all.
  - Fixed some dihedrals in sugars in Gromos53a5/6 working on the
    wrong atoms.
  - AmberGS force field is now based on Amber94 instead of Amber96.
  - Moved hydrogens in Charmm27 protein termini to separate charge
    groups and added ACE and CT3 residue types.
  - Many small fixes which avoid termination with fatal errors or
    crashes in mdrun and tools.
  - Many small updates to the manual pages of programs.

- Update to 4.5.4
  - Fixed pdb2gmx picking up force field from local instead of
    library directory
  - Made pdb2gmx vsite generation work again for certain His
    namings.
  - Fixed incorrect virial and pressure averages with certain
    nst... values (instantaneous values correct)
  - Fixed incorrect cosine viscosity output
  - New -multidir alternative for mdrun -multi option
  - Several minor fixes in analysis tools
  - Several updates to the program documentation

- Update to 4.5.3
  - Double precision energy file reading
  - CHARMM and GB issues
  - Support for Altivec (PowerPC) with CMake
  - Running binaries within the CMake build tree is now possible
  - Various other fixes

- Update to 4.5.1
  - fix bnc#642828 (CVE-2010-4001: Insecure use of LD_LIBRARY_PATH)
  See http://www.gromacs.org/About_Gromacs/Release_Notes/Version_4.5
  for a full list of changes
  - 2D decomposition support for PME: improved load balancing with
    up to 40% overall performance improvement for large systems.
  - Memory usage is improved for very large systems, allowing
    simulations of >100 million atoms.
  - Running on multi-core nodes now automatically uses thread-
    based parallelization.
  - GPU computing support
  - Check-pointing is made more secure:MD5sum are used to verify
    that all files are correctly in-place before a simulation is
    appended. Output file appending at continuation is turned on
    by default
  - Full Cmake support. Autoconf/automake will be deprecated after
    the final 4.5 release!
  - Full support for 7 AMBER force fields
  - Support for CHARMM27, including cmap for dihedrals
  - Efficient Generalized-Born implicit solvent support including
    the Still/HCT/OBC-models to compute the Born radii, a novel way
    of tabulating the generalized Born-interaction formula for
    greater speed, and optimized SSE-routines for both cut-off and
    all-vs-all simulations.
  - Support for nucleic acid simulations
  - Support for Velocity-Verlet integrators for reversible T- and
    P-coupling; MTTK pressure control integrators; Nose-Hoover
    chains
  - Support for Bennett acceptance ratio (BAR) free energy
    calculations
  - Decoupling group setup for free energy
  - File formats: All GROMACS tools can now read any VMD supported
    trajectory format, without converting trajectory first. (VMD
    is required)
  - g_rdf was a little bit enhanced that structure factors can be
    calculated for any system, by supplying the necessary data via
    sfactor.dat. Most of the common atomtypes are already contained,
    but everybody who needs more freedom can enhance the table
  - Library support for "dynamic index groups" based on textual
    selections (experimental feature). See the tool g_select, the
    included template.c, or Doxygen documentation for information on
    how to write analysis tools using the library. Existing tools
    have not (yet) been converted.
  - g_tune_pme: For a given number of processes or threads this tool
    systematically times mdrun with various numbers of PME-only nodes
    and determines which setting is fastest. It also checks whether
    performance can be enhanced by shifting load between the real and
    the reciprocal space part of the Ewald sum.
  - g_membed: a very convenient utility for embedding membrane
    proteins into equilibrated lipid bilayers

- read "/dev/urandom" instead of /dev/random

- fix build with automake 1.11

- remove static libraries and "la" files

- Fix buffer overflow (gcc static detection) in calcmu.c